The game that would eventually become Super 3D Noah's Ark was originally conceived as a licensed game based on the film Hellraiser, a movie that Wisdom Tree founder Dan Lawton was a great fan of. The player eventually comes across larger and more powerful slingshots, and flings coconuts and watermelon at the larger boss-like animals, such as Ernie the Elephant and Carl the Camel. There are secret levels, and shortcut levels as well. Noah's Ark includes secret passages, food, weapons and extra lives. The gameplay is aimed at younger children. Goats are also unable to open doors, while the other animals can.

The animals behave differently: goats, the most common enemy, will only kick Noah, while the other animals such as sheep, ostriches, antelopes and oxen will shoot spittle at him from a distance. Instead of killing Nazi soldiers in a castle, the player takes the part of Noah, wandering the Ark, using a slingshot to shoot sleep-inducing food at angry attacking animals, mostly goats, in order to render them unconscious. The game plays similarly to Wolfenstein 3D, but the graphics were changed to reflect a non-violent theme. Super 3D Noah's Ark plays similarly to Wolfenstein 3D, and utilizes the same game engine.

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